From owner-chemistry@ccl.net Fri Nov 6 17:27:01 2009 From: "Shikha Varma SVarma^^accelrys.com" To: CCL Subject: CCL: Homology modeling and loop refinement Message-Id: <-40629-091106162633-7095-7IhothXvfnZCTBFvu1gQSw]^[server.ccl.net> X-Original-From: Shikha Varma Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 6 Nov 2009 16:26:16 -0500 MIME-Version: 1.0 Sent to CCL by: Shikha Varma [SVarma%x%accelrys.com] Dear Werner, You can try MODELER for homology modeling and CHARMm based algorithm Looper= for loop refinement. Both methods are implemented in Accelrys Discovery S= tudio modeling package. MODELER program is developed by Andrej Sali (http://salilab.org/index.html)= and is the best homology modeling package available. It is used as the of= ficial model building program by CASP (http://predictioncenter.org/index.cg= i), a community organized Critical Assessment of techniques for protein Str= ucture Prediction. It is highly automated and has many unique features, su= ch as allowing you to create model including ligands, build multiple chain = protein with symmetry constraints, etc, to make the model building easy and= accurate. Looper (Spassov, V.Z., et al, Protein Engineering Design and Selection 2008= , 21(2), 91-100) is an algorithm developed at Accelrys and is a very fast a= nd accurate loop prediction method. It is based on the well known CHARMm (= CHARMM) simulation engine developed at Harvard university. The implementati= on of LOOPER algorithm in Loop Refinement protocol is based on CHARMm ene= rgy calculations and it is flexible to a choice of most of CHARMm forcefi= elds what allows the predicted structures to be used directly by other mode= ling protocols, such as MD simulations, pK predictions etc. Publications of interest: 1. Spassov, V. Z.; Yan, L. A fast and accurate computational approach to pr= otein ionization. Protein Sci. 2008, 17, 1955-1970.=20 2.Koska, J.; Spassov, V. Z.; Maynard, A. J.; Yan, L.; Austin, N.; Flook, P.= K.; Venkatachalam, C. M. Fully automated molecular mechanics based induced= fit protein-ligand docking method. J. Chem. Inf. Model. 2008, 48, 1965-197= 3.=20 3. Eswar, N.; Eramian, D.; Webb, B.; Shen, M. Y.; Sali, A. Protein structur= e modeling with MODELLER. Methods Mol. Biol. 2008, 426, 145-159.=20 4. Spassov, V.; Yan, L.; Flook, P. The dominant role of side-chain backbone= interactions in structural realization of amino acid code. ChiRotor: a sid= e-chain prediction algorithm based on side-chain backbone interactions. Pro= tein Sci. 2007, 16, 494-506.=20 5. Marti-Renom, M. A.; Madhusudhan, M. S.; Sali, A. Alignment of protein se= quences by their profiles. Protein Sci. 2004, 13, 1071-1087.=20 6. Li, L.; Chen, R.; Weng, Z. RDOCK: refinement of rigid-body protein docki= ng predictions. Proteins 2003, 53, 693-707.=20 Chen, R.; Li, L.; Weng, Z. ZDOCK: an initial-stage protein-docking algorith= m. Proteins 2003, 52, 80-87.=20 Morea, V.; Lesk, A.; Tramontano, A. Antibody modeling: implications for eng= ineering and design. Methods 2000, 20, 267-279.=20 7. Sali, A.; Pottertone, L.; Yuan, F.; van Vlijmen, H.; Karplus, M.; Evalua= tion of comparative protein modeling by MODELLER. Proteins 1995, 23, 318-32= 6. 8. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. = Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODEL= LER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Suppleme= nt 15, 5.6.1-5.6.30, 2006.=20 9. M.A. Marti-Renom, A. Stuart, A. Fiser, R. S=E1nchez, F. Melo, A. Sali. C= omparative protein structure modeling of genes and genomes. Annu. Rev. Biop= hys. Biomol. Struct. 29, 291-325, 2000.=20 A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of s= patial restraints. J. Mol. Biol. 234, 779-815, 1993.=20 10. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, = Protein Science 9. 1753-1773, 2000. Shikha Varma-O'Brien, Ph.D. Director, LS Modeling & Simulations Accelrys, Inc. 10188 Telesis Court, Suite 100 San Diego, CA 92121, USA Ph: +1 858 799 5607 Fax: +1 858 799 5100 =20 Stay Connected with Accelrys and the Scientific & Engineering Community Blog | Forum | Website | Support -----Original Message----- > From: owner-chemistry+shikha=3D=3Daccelrys.com_._ccl.net [mailto:owner-chemis= try+shikha=3D=3Daccelrys.com_._ccl.net] On Behalf Of Werner K werner.schroedi= nger-x-googlemail.com Sent: Wednesday, November 04, 2009 8:53 AM To: Shikha Varma Subject: CCL: Homology modeling and loop refinement Sent to CCL by: "Werner K" [werner.schroedinger^-^googlemail.com] Hi, what are in your opinion the best softwares, free and commercial, for prote= in homology modeling and loop refinement? Thanks WS -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt